|
| Status |
Public on May 10, 2014 |
| Title |
SK-HEP-1, 2T, mRNA (SOLID 3) |
| Sample type |
SRA |
| |
|
| Source name |
Liver cell line SK-HEP-1, Antrodia cinnamomea treated, 2 hours
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SK-HEP-1
treatment: Antrodia cinnamomea
time: 2 hours
|
| Treatment protocol |
Treated with 0.5 mg/ml Antrodia cinnamomea fruiting body ethanol extracts or 0.5 mg/ml DMSO.
|
| Growth protocol |
Cells were cultured in DMEM medium with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent. mRNA were isolated from total RNA samples by Poly(A) Purist-MAG kit.
SOLiD™ total RNA-seq kit for whole transcriptome libraries and small RNA libraries kits were used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard SOLiD™protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
mRNA; RNA-Seq
2T
Processed data file: Transcriptome.txt
|
| Data processing |
mRNA data used Galaxy web portal for abundance measurements. Sequenced reads were then trimmed for adaptor sequence, low-quality sequence or low-complexity mapped to hg19 with 2 mismatches using tophat and cufflinks for abundance measurement.
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009 (PMID 19528076). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text files. 'Transcriptome.txt' includes FPKM values for each mRNA sample; 'miRNA_solid5500.txt', 'miRNA_solid3.txt', and 'fCL_5500.txt' include TPM for each miRNA sample.
|
| |
|
| Submission date |
Jun 26, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
mike thang |
| Organization name |
Academia Sinica
|
| Department |
Genome Research Center
|
| Lab |
2L11
|
| Street address |
128 Academia Road, Section 2, Nankang
|
| City |
Taipei |
| State/province |
Taipei |
| ZIP/Postal code |
115 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL9442 |
| Series (1) |
| GSE48327 |
Global assessment of Antrodia cinnamomea induced microRNA and mRNA transcriptomic alterations in hepatocarcinoma cells |
|
| Relations |
| SRA |
SRX315245 |
| BioSample |
SAMN02214068 |
